1KQF | pdb_00001kqf

FORMATE DEHYDROGENASE N FROM E. COLI

PDB DOI: https://doi.org/10.2210/pdb1KQF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2002-01-05 Released: 2002-03-15
Deposition Author(s): Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.177 (Depositor), 0.182 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.

Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.

(2002) Science 295: 1863-1868

PubMed: 11884747 Search on PubMed
DOI: https://doi.org/10.1126/science.1068186
Primary Citation Related Structures:
1KQF, 1KQG

PubMed Abstract:
The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.

Organizational Affiliation

Division of Biomedical Sciences, Imperial College, London SW7 2AZ, UK.

Macromolecule Content

Total Structure Weight: 176.81 kDa
Atom Count: 13,989
Modeled Residue Count: 1,487
Deposited Residue Count: 1,526
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT	A	1,015	Escherichia coli	Mutation(s): 0 EC: 1.2.1.2 (PDB Primary Data), 1.17.5.3 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P24183 (Escherichia coli (strain K12)) Explore P24183 Go to UniProtKB: P24183
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24183
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT	B	294	Escherichia coli	Mutation(s): 0 EC: 1.2.1.2 Membrane Entity: Yes
UniProt
Find proteins for P0AAJ3 (Escherichia coli (strain K12)) Explore P0AAJ3 Go to UniProtKB: P0AAJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AAJ3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT	C	217	Escherichia coli	Mutation(s): 0 EC: 1.2.1.2 Membrane Entity: Yes
UniProt
Find proteins for P0AEK7 (Escherichia coli (strain K12)) Explore P0AEK7 Go to UniProtKB: P0AEK7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	L [auth C], M [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain L [auth C] Focus chain M [auth C]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
6MO Query on 6MO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.177 (Depositor), 0.182 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203	α = 90
b = 203	β = 90
c = 203	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-03-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-03-15
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2014-02-19
Changes: Atomic model, Structure summary
Version 1.4: 2014-08-06
Changes: Derived calculations, Structure summary
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations